Rokugan shadowlands - magic item use, ability damage, and others

[ShurikVch]

Naga seems cool enough but no idea how to make it into the plot with a Naga character, are they friends with some clan like the Nezumi are with the Crab?

Naga and the Crab

And wow, I didn't know that there were Shadowlands-subtype player characters - aren't all these shadowland creatures controlled by Fu-leng? Or can they actually be a part of the empire?

Well, Bakemono, Ogre (Shadowlands), and Tsuno are explicitly playable in the 3.0 Oriental Adventures

But for the "part of the empire"... Try the Spider Clan?